The story starts immediately after the events of the previous title ending with Michael Ford waking up after escaping the exploded Trust base on an off-shore oil rig. As Ford regains consciousness he is ambushed by two workers. As Ford continues through the complex, the surrounding areas and the complex itself are attacked by the Leviathan, an ancient sea monster. After Ford makes it to the top of the rig, he begins to fight the Leviathan. Ford uses the Trust’s mounted machines around the oil rig to attack the Leviathan and eventually spears it with a harpoon.

Ford must use Atlantis, a ship that Enlil, also known as John Adams in The Conduit’s universe, came to Earth in to go to various areas around the globe. It is revealed that aliens have secretly been controlling parts of Earth and Ford must gain their trust in the fight against the Trust.